The report was generated using the JSEQ_scRNAseq single-cell analysis pipeline. For more information, please visit: https://github.com/jkubis96/JSEQ_scRNAseq


1 Analysis Configuration Parameters

Parameter Value
mt_per 25
scale_factor 1e+06
n_features 2000
c_res 0.5
heterogeneity deg
mt_cssg FALSE
m_val 0.05
top_m 50
max_genes 1000
max_combine 1000
loss_val 0.05
s_factor 0.8
p_bin 0.05
drop TRUE
min_c 10

The parameters above were used during the current analysis.
If you need to apply different analysis conditions, modify the parameters in the configuration file.

Parameters description:

  • mt_per
    Maximum percentage of mitochondrial genes per cell.
    Default: 25%
  • down
    Lower threshold for the number of genes per cell.
    Default: NA (automatically computed if NA)
  • up
    Upper threshold for the number of genes per cell.
    Default: NA (automatically computed if NA)
  • scale_factor
    Scale factor used for data normalization.
  • n_features
    Number of variable features to detect for clustering.
  • c_res
    Clustering resolution — higher values produce more clusters.
  • heterogeneity
    Method for estimating cluster heterogeneity.
    Options: var (within-cluster variance), deg (deregulated gene profiles).
    Default: deg
  • mt_cssg
    Whether to include mitochondrial genes when creating subclasses and subtypes.
    Options: TRUE, FALSE.
    Default: FALSE
  • m_val
    Maximum p-value threshold for marker detection in advanced subtype analyses.
    Default: 0.05
  • top_m
    Maximum number of top markers used for naming clusters based on effect size metrics.
    Default: 50
  • max_genes
    Maximum number of input genes considered in cluster heterogeneity discovery.
    Default: 1000
  • max_combine
    Maximum number of initial combinations for each iteration during heterogeneity discovery.
    Default: 1000
  • loss_val
    Assigned value for potentially unclassified cells within a cluster.
  • s_factor
    Maximum split factor for gene occurrence in heterogeneity discovery (0.2–1).
    Default: 0.8
  • p_bin
    Minimum cell proportion required for population presence based on binomial test p-value.
    Default: 0.05
  • min_c
    Minimum cell proportion required for population presence as defined by the user (independent of binomial test).
    Default: 10
  • drop
    Boolean indicating whether to drop non-significant subtypes based on p_bin and min_c.
    Default: TRUE

The configuration file is available in the directory:
JSEQ_scRNAseq/requirements_file/config_file.conf

Additional configuration files for other analysis steps can also be found in:
JSEQ_scRNAseq/requirements_file

For more information, please visit:
https://github.com/jkubis96/JSEQ_scRNAseq



2 Cell content analysis

2.1 Ratio of number of genes to counts

2.2 Number of genes and counts per cell

2.3 Percentage of ribosomal and mitochondrial genes [%]



3 Quality control of cell content

3.1 Genes per cell content & thresholds

3.2 Genes upper & lower thresholds per cell

3.3 Number of cells across different stages of analysis



4 Gene expression analysis across cells

4.1 Top highly variable genes in the dataset



5 Princilpe component selection

5.1 ElbowPlot - principal components cutoff

5.2 JackStrawPlot - PC significance



6 Cells clustering

6.1 UMAP clusters



7 Subclasses identification based on marker genes

7.1 PCA cisualization of subclasses

7.2 UMAP visualization of subclasses

7.3 Subclasses - cell composition


7.4 Subclasses markers - top 25


Top 25 merkers
genes pct_occurrence esm avg_logFC p_val cluster p_adj_bf p_adj_bh subclass
MT-RNR2 0.9480519 0.2943721 0.1088171 0.0000000 0 0.0000000 0.0000000 TEG ZFPM2 ENSG00000233755
PPFIBP2 0.0519481 0.1604065 1.2272448 0.0230524 0 0.2766286 0.1383143 TEG ZFPM2 ENSG00000233755
ENSG00000233755 0.0930736 0.1448644 0.7404038 0.0463976 0 0.5567715 0.1391929 TEG ZFPM2 ENSG00000233755
MT-ND4L 0.4004329 0.0325188 0.0568023 0.0359697 0 0.4316363 0.1391929 TEG ZFPM2 ENSG00000233755
PNISR 0.5523466 1.1303595 2.3654247 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SRSF11 0.4873646 1.1180884 2.6664348 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
RBM25 0.5306859 1.0064723 2.1314647 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
ARGLU1 0.4584838 0.9865719 2.4018108 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SETD5 0.3790614 0.9864712 2.9526072 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
LUC7L3 0.5956679 0.9764462 1.7980896 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HNRNPA2B1 0.4945848 0.9211209 2.0289638 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SRRM2 0.3285199 0.8697239 2.8167677 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HNRNPR 0.4620939 0.8639703 2.0043969 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
PRRC2C 0.5126354 0.8639157 1.8199530 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HNRNPD 0.4187726 0.8598310 2.1713607 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
BPTF 0.3718412 0.8493818 2.4042235 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
TXNIP 0.4981949 0.8373820 1.7793625 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
ZRANB2 0.3285199 0.8223846 2.5957504 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
DDX5 0.4296029 0.8172000 1.9875079 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
TIA1 0.2418773 0.8120068 3.4977910 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HSP90AB1 0.6534296 0.8035374 1.2849250 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
HNRNPDL 0.4981949 0.7992691 1.6882866 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
NKTR 0.2707581 0.7815232 2.8901096 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
PAFAH1B1 0.3971119 0.7780055 2.0036973 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SON 0.3790614 0.7681067 2.0704723 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
PNN 0.3357401 0.7631730 2.2836210 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
DDX17 0.4332130 0.7570656 1.7915320 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SRRM1 0.4332130 0.7509675 1.7794081 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
CEP95 0.2093863 0.7463068 3.5299231 0.0000000 1 0.0000000 0.0000000 TEG ZFPM2 MALAT1
SUZ12 0.8571429 0.6521914 0.5823289 0.0000000 2 0.0000000 0.0000000 TEG ZFPM2 KCNG4
CHST11 0.4081633 0.6284434 1.2635037 0.0000000 2 0.0000007 0.0000003 TEG ZFPM2 KCNG4
KCNG4 0.1530612 0.5739845 2.1895728 0.0000002 2 0.0000273 0.0000091 TEG ZFPM2 KCNG4
DOCK4 0.1122449 0.4974462 2.2032658 0.0000184 2 0.0021525 0.0005381 TEG ZFPM2 KCNG4
ANKRD30BL 0.0816327 0.4840782 2.5935197 0.0000234 2 0.0027389 0.0005478 TEG ZFPM2 KCNG4
SLC12A2 0.2244898 0.4783686 1.3935272 0.0000329 2 0.0038487 0.0006414 TEG ZFPM2 KCNG4
IL1F10 0.0612245 0.4505006 2.8776636 0.0000454 2 0.0053174 0.0007596 TEG ZFPM2 KCNG4
ENSG00000254840 0.2244898 0.4355335 1.2642208 0.0001337 2 0.0156384 0.0019548 TEG ZFPM2 KCNG4
LINC01716 0.0510204 0.3978794 2.7295115 0.0005508 2 0.0644419 0.0053702 TEG ZFPM2 KCNG4
LINC01681 0.0816327 0.3918819 2.1046915 0.0003642 2 0.0426056 0.0042606 TEG ZFPM2 KCNG4
RFX2 0.3673469 0.3751707 0.7883006 0.0003328 2 0.0389390 0.0042606 TEG ZFPM2 KCNG4
SMYD3.var1 0.0612245 0.3474395 2.0923919 0.0050499 2 0.5908436 0.0365260 TEG ZFPM2 KCNG4
APOH 0.1632653 0.3458943 1.2131972 0.0029723 2 0.3477640 0.0248403 TEG ZFPM2 KCNG4
NOTCH2 0.0510204 0.3197307 2.1900200 0.0048527 2 0.5677616 0.0365260 TEG ZFPM2 KCNG4
MAP3K10 0.0714286 0.2993358 1.6681662 0.0130372 2 1.0000000 0.0847419 TEG ZFPM2 KCNG4
UNC13C 0.0510204 0.2933437 2.0661576 0.0053072 2 0.6209426 0.0365260 TEG ZFPM2 KCNG4
LINC00486 0.2040816 0.2705040 0.8274494 0.0146749 2 1.0000000 0.0903667 TEG ZFPM2 KCNG4
NMNAT2 0.0612245 0.2680150 1.6439134 0.0230783 2 1.0000000 0.1285791 TEG ZFPM2 KCNG4
IQSEC1 0.0510204 0.2624504 1.7138774 0.0492255 2 1.0000000 0.2206001 TEG ZFPM2 KCNG4
ENSG00000250961 0.0816327 0.2487368 1.3225915 0.0248751 2 1.0000000 0.1293415 TEG ZFPM2 KCNG4
ENSG00000233755 0.1326531 0.2482931 1.0022172 0.0254261 2 1.0000000 0.1293415 TEG ZFPM2 KCNG4
ZFPM2 0.2653061 0.2434642 0.6203788 0.0228340 2 1.0000000 0.1285791 TEG ZFPM2 KCNG4
TRIM71 0.0612245 0.2357298 1.4377222 0.0485614 2 1.0000000 0.2206001 TEG ZFPM2 KCNG4
MT-ND4 0.5918367 0.2074306 0.2697502 0.0004226 2 0.0494445 0.0044950 TEG ZFPM2 KCNG4
MT-RNR2 0.9591837 0.1917874 0.0753420 0.0021947 2 0.2567854 0.0197527 TEG ZFPM2 KCNG4
HS6ST3 0.5614035 2.9228573 4.6567511 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
DOCK9 0.6666667 2.6089908 3.6496134 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000254840 0.7192982 2.4793407 3.3678033 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
CYRIB 0.5087719 2.2168804 3.8573725 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
RFX2 0.8947368 2.1067320 2.3835340 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ANKFN1.var1 0.4912281 2.0383039 3.6595689 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
LINC00486 0.6666667 2.0056607 2.9108364 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
APOH 0.5087719 1.8847868 3.2672138 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ZFPM2 0.7719298 1.8332059 2.4084283 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
CHST11 0.7894737 1.8286630 2.3561399 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000240963 0.2631579 1.8127933 4.8245490 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
UBE2E2.var1 0.5789474 1.6353313 2.6578025 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
PHF20 0.3333333 1.6347562 3.6764777 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
TYW1B.var1 0.2105263 1.5759874 4.9236294 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
WDR88 0.2807018 1.5756224 4.0407607 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
BACH2 0.3508772 1.5001488 3.3491957 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
LINC00536.var1 0.1929825 1.4237528 4.6923754 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
SLC12A2 0.4736842 1.4225603 2.6176585 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000279465 0.2982456 1.3899192 3.3768871 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
RIOX2 0.1578947 1.3752147 5.0779323 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000288011 0.2280702 1.3710866 4.0603534 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
LINC02814 0.2280702 1.3645709 3.9046559 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000226197 0.1754386 1.3451350 4.6182786 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
ENSG00000246225 0.2280702 1.3323424 3.7632144 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9
DUXAP10 0.1929825 1.3200506 4.0979211 0.0000000 3 0.0000000 0.0000000 TEG ZFPM2 DOCK9


7.5 Heatmap of cell subclasses - log(CPM + 1)

7.6 Heatmap of cell subclasses - scale(log(CPM + 1))




8 Subtypes identification based on CSSG genes

8.1 UMAP visualization


8.2 Subtypes - cell composition


8.3 Subtypes markers - top 25


Top 25 markers
genes pct_occurrence esm avg_logFC p_val subtype p_adj_bf p_adj_bh cluster
PPFIBP2 1.0000000 5.8573977 5.0510830 0.0000000 TEG ZFPM2 ENSG00000233755 - PPFIBP2 0.0000000 0.0000000 0
ENSG00000233755 1.0000000 5.0523329 4.4536751 0.0000000 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.0000000 0.0000000 0
MPP7.var1 0.2500000 0.8360283 2.3210410 0.0006096 TEG ZFPM2 ENSG00000233755 - PPFIBP2 0.0347495 0.0173747 0
GNAI1 0.1500000 0.8266246 2.8958131 0.0016711 TEG ZFPM2 ENSG00000233755 - PPFIBP2 0.0952512 0.0317504 0
LMBRD1 0.1500000 0.6580889 2.2642754 0.0260400 TEG ZFPM2 ENSG00000233755 - PPFIBP2 1.0000000 0.2473799 0
KCNG4 0.1627907 0.6379853 2.3419154 0.0001590 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.0027023 0.0009008 0
ENSG00000243199 0.2000000 0.5741576 1.7923164 0.0259656 TEG ZFPM2 ENSG00000233755 - PPFIBP2 1.0000000 0.2473799 0
KCNG4 0.1500000 0.5433497 2.0647710 0.0239265 TEG ZFPM2 ENSG00000233755 - PPFIBP2 1.0000000 0.2473799 0
PPM1H.var1 0.1162791 0.4420487 1.8733241 0.0187015 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.3179248 0.0794812 0
MPP7.var1 0.1395349 0.4075389 1.5667299 0.0264723 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.4500292 0.0900058 0
MT-RNR2 0.9534884 0.3529472 0.1439651 0.0000058 TEG ZFPM2 ENSG00000233755 - ENSG00000233755 0.0000986 0.0000493 0
RBM25 0.5306859 1.1088582 3.1600885 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
SRSF11 0.4873646 1.1065830 3.9575185 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
HSP90AB1 0.6534296 1.0351984 1.8452727 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
LUC7L3 0.5956679 1.0068706 2.0800146 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
HNRNPA2B1 0.4945848 0.9703982 2.7260866 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
PNISR 0.5523466 0.9380181 2.0984619 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
PRRC2C 0.5126354 0.8955268 2.2089133 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
RPL23 0.4981949 0.8816947 2.2293477 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
TXNIP 0.4981949 0.8722371 2.1973544 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
MALAT1 1.0000000 0.8630070 0.0856148 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
HNRNPR 0.4620939 0.8515161 2.3679298 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
SETD5 0.3790614 0.8372310 3.2396141 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
YBX1 0.6425993 0.8210745 1.3645736 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000036 0.0000001 1
SON 0.3790614 0.8167009 3.0301491 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
RPL24 0.4584838 0.7993041 2.1432523 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
HNRNPDL 0.4981949 0.7871019 1.8504950 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
ARGLU1 0.4584838 0.7848145 2.0683080 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
RPS8 0.5956679 0.7726763 1.3880136 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000045 0.0000001 1
NCL 0.4332130 0.7707967 2.1775199 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
DDX5 0.4296029 0.7660591 2.1735043 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
FNBP1L 0.3790614 0.7637418 2.6240189 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
ZRANB2 0.3285199 0.7622448 3.3410808 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
RPL14 0.4801444 0.7586489 1.8283251 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
ZNF638 0.3249097 0.7551620 3.3297034 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
DDX17 0.4332130 0.7538637 2.0868450 0.0000000 TEG ZFPM2 MALAT1 - MALAT1 0.0000000 0.0000000 1
CHST11 1.0000000 1.7715617 1.8814283 0.0000000 TEG ZFPM2 KCNG4 - CHST11 0.0000000 0.0000000 2
RFX2 1.0000000 1.6204503 1.7126613 0.0000000 TEG ZFPM2 KCNG4 - RFX2 0.0000000 0.0000000 2
KCNG4 0.2400000 0.9986802 2.8422320 0.0000034 TEG ZFPM2 KCNG4 - RFX2 0.0002457 0.0001229 2
OLFM2 0.1200000 0.9875768 3.9219536 0.0000168 TEG ZFPM2 KCNG4 - CHST11 0.0012409 0.0005895 2
PRDX3 0.1200000 0.9522948 3.7088663 0.0000726 TEG ZFPM2 KCNG4 - CHST11 0.0053698 0.0011388 2
ENSG00000287277 0.1200000 0.9056296 3.6055735 0.0000769 TEG ZFPM2 KCNG4 - CHST11 0.0056940 0.0011388 2
APBB2.var1 0.1200000 0.7915785 3.0190525 0.0026826 TEG ZFPM2 KCNG4 - CHST11 0.1985142 0.0183900 2
FAM217B 0.1200000 0.7760776 3.0604234 0.0014143 TEG ZFPM2 KCNG4 - CHST11 0.1046580 0.0133561 2
PSMC4 0.1200000 0.7677183 3.0421751 0.0014439 TEG ZFPM2 KCNG4 - CHST11 0.1068484 0.0133561 2
PDE1C.var2 0.1600000 0.7387529 2.6052553 0.0009081 TEG ZFPM2 KCNG4 - RFX2 0.0662914 0.0132583 2
CFAP251 0.1200000 0.7038845 2.8365546 0.0027336 TEG ZFPM2 KCNG4 - CHST11 0.2022896 0.0183900 2
NOTCH2 0.1200000 0.6999009 2.8973582 0.0015362 TEG ZFPM2 KCNG4 - RFX2 0.1121391 0.0186898 2
LINC01681 0.1600000 0.6565175 2.3951640 0.0019482 TEG ZFPM2 KCNG4 - CHST11 0.1441643 0.0160183 2
FGF14.var1 0.1200000 0.6336429 2.6228657 0.0050368 TEG ZFPM2 KCNG4 - CHST11 0.3727254 0.0310605 2
SUZ12 0.9200000 0.6154919 0.4631502 0.0000239 TEG ZFPM2 KCNG4 - CHST11 0.0017685 0.0005895 2
ACACA 0.1200000 0.6145135 2.5288983 0.0081171 TEG ZFPM2 KCNG4 - CHST11 0.6006618 0.0462048 2
RNF11 0.1200000 0.5992690 2.4460914 0.0122911 TEG ZFPM2 KCNG4 - CHST11 0.9095444 0.0649675 2
CCDC59 0.1600000 0.5482939 1.8942742 0.0273406 TEG ZFPM2 KCNG4 - RFX2 1.0000000 0.2851236 2
ENSG00000223720 0.1200000 0.5288439 2.1660477 0.0310382 TEG ZFPM2 KCNG4 - CHST11 1.0000000 0.1351075 2
SLC12A2 0.3200000 0.5031046 1.2091560 0.0176591 TEG ZFPM2 KCNG4 - CHST11 1.0000000 0.0816736 2
MT-RNR2 1.0000000 0.5014454 0.2040283 0.0004337 TEG ZFPM2 KCNG4 - CHST11 0.0320962 0.0053494 2
ENSG00000288011 0.1200000 0.4605178 1.9943422 0.0353197 TEG ZFPM2 KCNG4 - CHST11 1.0000000 0.1452034 2
LINC01681 0.1200000 0.4547029 1.9804388 0.0337078 TEG ZFPM2 KCNG4 - RFX2 1.0000000 0.3075841 2
ENSG00000250961 0.1200000 0.4435947 1.9158981 0.0444826 TEG ZFPM2 KCNG4 - RFX2 1.0000000 0.3608032 2
SUZ12 0.8400000 0.4059101 0.3302442 0.0005535 TEG ZFPM2 KCNG4 - RFX2 0.0404030 0.0101007 2
HS6ST3 0.6400000 2.8083795 4.4863348 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
DOCK9 0.7600000 2.5716783 3.3446878 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000254840 0.7600000 2.1490569 2.8716808 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
RFX2 1.0000000 2.1154226 2.0394933 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
LINC00486 0.6800000 1.7796119 2.5842787 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
CYRIB 0.5000000 1.7586755 3.3359301 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ANKFN1.var1 0.4600000 1.6091175 3.2236735 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ZFPM2 0.7800000 1.6022997 2.0303586 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
APOH 0.5200000 1.5681949 2.7962511 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
UBE2E2.var1 0.6200000 1.5560982 2.4346618 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000240963 0.3000000 1.4812872 4.1026400 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000226197 0.2000000 1.3261443 5.2869060 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000279465 0.3400000 1.3202787 3.2119882 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
WDR88 0.2800000 1.2716937 3.5990320 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
PHF20 0.3600000 1.2613889 2.9082193 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
CHST11 0.7600000 1.2586773 1.5967919 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
SUZ12 0.9800000 1.2239267 0.7797739 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000223393 0.6600000 1.2196831 1.7456567 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000288011 0.2400000 1.1912343 3.8843482 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
RIOX2 0.1600000 1.1543542 5.0747074 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
TYW1B.var1 0.2000000 1.1370017 4.0775352 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
ENSG00000246225 0.2600000 1.1215573 3.2035191 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
LINC02814 0.2600000 1.1205603 3.2522165 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
TRIM71 0.2200000 1.1192474 3.7124839 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3
MAP1LC3BP1 0.1800000 1.1115284 4.2686929 0.0000000 TEG ZFPM2 DOCK9 - RFX2 0.0000000 0.0000000 3


8.4 Heatmap of cell subtypes - log(CPM + 1)

8.5 Heatmap of cell subtypes - scale(log(CPM + 1))




9 Disclaimer

The analysis was performed through the non-profit and open-source pipeline JSEQ_scRNAseq. Remember, in silico analysis must be validated in vitro or in vivo. For more information, visit GitHub or contact us. JSEQ_scRNAseq was created at the Institute of Bioorganic Chemistry, Polish Academy of Sciences.